I would like to annotate a .vcf file and also summarize possible effects variants can have on genes (stop codon, amino acid changes, etc.)
It seems that is what the output of SnpEff can provide (http://snpeff.sourceforge.net/SnpEff.html).
I have uploaded a .vcf file, .fasta file, and .gff3 file to Galaxy.
I try the program on the leftbar of Galaxy (SnpEff: Variant effect and annotation). For the "Sequence Changes" field, I put the .vcf file. For the "Input Format" field, I put VCF. For the "Genome" field, it seems there are only two hard-coded choices to choose from. My species is Seriola, which is not listed.
My question is: Do I have the necessary files in the necessary places to run SnpEff on Galaxy? If not, is there any tool on Galaxy that I can use to annotate .vcf file and summarize effects the variants can have on genes?
Thank you for any advice..!